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VCY Gene

protein-coding   GIFtS: 38
GCID: GC0YM016098

Variable Charge, Y-Linked

(Previous names: variable charge, Y chromosome)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Variable Charge, Y-Linked1 2     VCY12
BPY12 3 5     Basic Protein On Y Chromosome, 12
Variable Charge, Y Chromosome1 2     Testis-Specific Basic Protein On Y, 12
Basic Charge, Y-Linked 12 3     Testis-Specific Basic Protein Y 12
Variably Charged Protein Y2 3     BPY1B3
VCY1A2 3     

External Ids:    HGNC: 126681   Entrez Gene: 90842   Ensembl: ENSG000001298647   OMIM: 4000125   UniProtKB: O145983   

Export aliases for VCY gene to outside databases

Previous GC identifers: GC0YP015485 GC0YM015407 GC0YM015106 GC0YP014607 GC0YP014678 GC0YP016169 GC0YM010741


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for VCY Gene:
The protein encoded by this gene is a member of a family of human VCX/Y genes. This gene family has multiple
members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. Members of the VCX/Y
family share a high degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in
X-linked members but occurs only once in Y-linked members. VCX/Y genes encode small and highly charged proteins
of unknown function. This gene encodes a small, positively charged protein. The presence of a putative bipartite
nuclear localization signal suggests that this gene encodes a nuclear protein. The genome has two identical
copies of this gene within a palindromic region; this record represents the more centromeric copy. (provided by
RefSeq, Jul 2008)

GeneCards Summary for VCY Gene:
VCY (variable charge, Y-linked) is a protein-coding gene. Diseases associated with VCY include y chromosome infertility, and gonadoblastoma. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot: VCY1_HUMAN, O14598
Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000024.10  NT_011875.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the VCY gene promoter:
         POU2F2 (Oct-2.1)   POU2F2   POU2F2C   POU2F1   POU2F1a   FOXO1a   NF-Y   POU2F2B   CBF(2)   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VCY


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Yq11.221   Ensembl cytogenetic band:  Yq11.221   HGNC cytogenetic band: Yq11.221

VCY Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VCY gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YM016098:  view genomic region     (about GC identifiers)

Start:
16,097,652 bp from pter      End:
16,098,393 bp from pter
Size:
742 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: VCY1_HUMAN, O14598 (See protein sequence)
Recommended Name: Testis-specific basic protein Y 1  
Size: 125 amino acids; 12917 Da

Explore the universe of human proteins at neXtProt for VCY: NX_O14598

Explore proteomics data for VCY at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See VCY Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004670.1  
    ENSEMBL proteins: 
     ENSP00000250825  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR026653 VCX/VCY1

    Graphical View of Domain Structure for InterPro Entry O14598

    ProtoNet protein and cluster: O14598

    UniProtKB/Swiss-Prot: VCY1_HUMAN, O14598
    Similarity: Belongs to the VCX/VCY family


    VCY for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VCY1_HUMAN, O14598
    Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

         Genatlas biochemistry entry for VCY:
    variable charge X/Y,basic protein on chromosome Y,1,testis specific,in a AZF deleted region

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VCY
    Interactions:

        Search GeneGlobe Interaction Network for VCY

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for VCY (VCY1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for VCY gene: 
    NM_004679.2  

    Unigene Cluster for VCY:

    Variable charge, Y-linked
    Hs.632284  [show with all ESTs]
    Unigene Representative Sequence: AF000979
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000250825(uc004ftc.3)
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    Additional mRNA sequence: 

    AF000979.1 BC096729.1 

    2 DOTS entries:

    DT.120654203  DT.443460 

    Selected AceView cDNA sequences (see all 43):

    AI917448 AI672566 AI634041 BF478074 AW193704 BF508070 AF000979 NM_181880 
    BF059317 AI650513 AI611655 AA496066 BX281130 AA759284 AI621240 AI809702 
    AW303648 AI809663 NM_004679 BC056508 AA393129 AA357797 AI963982 AI917301 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VCY expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    VCY Expression
    About this image

    VCY Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VCY Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.632284

    UniProtKB/Swiss-Prot: VCY1_HUMAN, O14598
    Tissue specificity: Expressed exclusively in testis

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of human and chimp.

    Orthologs for VCY gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia LOC7420751 variable charge X-linked protein 3B-like 95.69(n)
    88.79(a)
      742075  XM_003318999.2  XP_003319047.2 


    ENSEMBL Gene Tree for VCY (if available)
    TreeFam Gene Tree for VCY (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VCY gene
    VCY1B1 2  VCX21 2  VCX3B2  VCX2  VCX3A2  ENSG000002680802  
    5 SIMAP similar genes for VCY using alignment to 2 protein entries:     VCY1_HUMAN (see all proteins):
    VCY1B    VCX2    VCX3A    VCX    VCX3B

    VCY for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for VCY:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv469834CNV Gain16826518

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VCY
    DNA2.0 Custom Variant and Variant Library Synthesis for VCY

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 400012    OMIM disorders: --

    4 diseases for VCY:    
    About MalaCards
    y chromosome infertility    gonadoblastoma    x-linked ichthyosis    infertility

    1 disease from the University of Copenhagen DISEASES database for VCY:
    X-linked ichthyosis

    VCY for disorders           About GeneDecksing


    Export disorders for VCY gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for VCY gene integrated from 10 sources:
    (articles sorted by number of sources associating them with VCY)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Functional coherence of the human Y chromosome. (PubMed id 9381176)1, 2, 3 Lahn B.T. and Page D.C. (Science 1997)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2 Skaletsky H.... Page D.C. (Nature 2003)
    4. A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family. (PubMed id 17342728)1 Hansen M.A....Leffers H. (Mol. Reprod. Dev. 2008)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. (PubMed id 10607842)1 Lahn B.T. and Page D.C. (Hum. Mol. Genet. 2000)
    7. Toward a complete human genome sequence. (PubMed id 9847074)1 Sulston J.E. and Waterston R. (Genome Res. 1998)
    8. Y Chromosome Infertility (PubMed id 20301513)1 Pagon R.A....Stephens K. (1993)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9084 HGNC: 12668 AceView: VCY.1 Ensembl:ENSG00000129864 euGenes: HUgn9084
    ECgene: VCY H-InvDB: VCY

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VCY Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VCY gene:
    Search GeneIP for patents involving VCY

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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